Parallel Universe 2 - Eggman's Invasion
by AngryComet48
Summary: The sequel to Parallel Worlds. After 6 months of preparations, Eggman finally comes back to conquer the world, but things don't go according to plan for Sonic, Tails, and Shadow. Can Sonic save the world before it's too late?
1. Thrown into Chaos

**Here we go guys and gals. The part 2 of Parallel Universe. Is everyone ready for this? Please take a seat, and please enjoy.**

**Disclaimer: I own nothing but the story**

Parallel Universe 2: Eggman's Invasion: Chapter 1: Thrown into Chaos

-Sonic's POV-

I watch as the green portal glows and slowly gets bigger. I look to my right to see Shadow in a fighting stance, then I look to my left to see the same for Tails.

"Alright guys, here he comes… Get ready." Tails pushes a button on her bracelet, enhancing her ability to use the Chaos Emeralds. I look back at the portal to see a giant battleship coming out, along with many other smaller ones.

"Okay," I say, building up energy in the 7 Chaos Emeralds we had collected. "Go!" I feel the raw energy of the gemstones surging through my body as I start to levitate. I look over to Shadow to see that he's become a golden color. I look at Tails and see that she's now glowing silver. The three of use immediately fly up and start wreaking havoc upon Eggman's fleet, destroying any ships that dare cross our paths.

"Guys, I see the entrance to big one!" I hear Tails say, and I see the hatch that she's pointing at.

"Alright then, Chaos Control!" I yell, teleporting Tails, Shadow, and I in front of the door. I kick the door down and we start flying through the corridors.

"Well, if it isn't Sonic, Shadow, and my traitor daughter!" I glance around and locate a monitor with Eggman on it. "You may think that you have final victory in your hands… But guess again!" He moves, revealing a white hedgehog connected to some kind of machine.

"Silver?" I hear Shadow ask, somewhat confused. "Why do you have Silver?"

"Because, with his power and the combined help of the Sol Emeralds," He smiles maliciously. "I can prevent any of this from happening."

"Nice try, but it's too late." I smile cockily.

"Huh? How?"

"Because we're right outside your lab." I kick down a metal door. "Game over Egg-head." Eggman frowns, then presses a button, causing a machine to descend over us.

"I believe this is checkmate for you guys…" His smile returns. "Permanently." The machine shoots purple energy onto us, draining the energy of the Chaos Emeralds. I feel power leaving me and see the same happening to Shadow and Tails.

"Nope! You can't stop us completely!" Tails yells, pressing a button on the bracelet. Negative energy surges through my body as if I'm going Dark, except for the fact that I remain in complete control of my mind. I look and see Shadow transform as well, with his red coloring turning black and his eyes turning black, yet not disappearing. Tails' normally yellow fur turns black and her eyes also become black orbs.

"Eh? What is the meaning of this?!" Eggman yells with obvious confusion written on his face.

"You see," Tails starts. "During the six months of your absence, I was able to figure out how to use the Chaos Emeralds' leftover negative energy and control it, allowing us to-"

"Yeah yeah yeah, that's enough, prepare for the end!" Eggman pulls a lever, creating a portal in front of us. I note Silver and the Sol Emeralds glowing. I refocus on the portal, which now is pulling us in with intense force. I secure a hold on a metal pole, while Shadow and Tails grab a metal column. "Now…" I hear the doctor muse. "I just need my greatest enemy to fall in, but how will I do that?" He pulls another lever. "I know! I'll just increase the intensity of the vacuum!" The increased suction breaks my grip on the pole, and I feel like time is slowing down. I see Shadow and Tails with looks of horror on their faces and Eggman laughing triumphantly. I close my eyes and allow myself to be pulled in after realizing my hopeless position.

I wake up with a start in my bed, trying to figure out why I have a nasty headache. I get up and clumsily make my way downstairs.

"Tails?" I shout. "Do we have any headache-" I notice the once cluttered workshop abandoned and empty. "-medicine?" I quickly rush downstairs and look around frantically for any traces of my best friend. I notice an image of Tails on the TV screen and rush to it to find out what's going on.

"The Chaos Emerald's theft from the Mobian Wonders museum was most likely played out by Miles Prower, Dr. Eggman's daughter." A white squirrel is reporting. "More investigating will be put into this case, as there is more to uncover…" I collapse onto the couch.

"What?" I ask aloud. "What did Eggman do?" Worried, I rush to the door and look outside. "Everything looks normal… Let's see if any of my other friends are okay!" I start running towards Station Square.

I arrive and see a pink hedgehog walking along on the sidewalk.

"Ames!" Shout, happy that at least one of my friends is safe. "Over here!" Amy slowly turns around and locks eyes with me slowly. She then quickly runs the other direction.

"Police! Sonic the hedgehog is here!" She calls. "Somebody help me!"

"Huh?" I scratch my head, confused.

"Stop in the name of the law!" I see several police cars parking in front of me. "You will not terrorize this city any further!"

"What the-" A bullet barely misses me. "Crap, I've got to get out of here, and fast!" I turn to run, only to be blocked by a black hedgehog.

"Hold it right there." Shadow snarls. "You will not go any further. You have cause this city and the people of Mobius enough harm, and I will personally put a stop to it."

"Not you too Shadow…" I groan. "Will somebody please tell me what's going on?" Shadow charges and I sidestep, causing him to tackle a police car. I use my diversion and quickly run away, making sure that I'm not followed. "What is up with everybody today?" I ask myself aloud. "Everyone's acting like I'm a big international criminal!" Sudden memories of Eggman's portal flood into my mind. "What the-?" I stop running. "Eggman must've changed the past! He found a way to make my life miserable, allowing him to take over!" I collapse under a tree. "If only I had some friends though…" I sigh sadly.

"Well, it seems you're in luck Honey." I look up to see Rouge hanging upside down in the tree, facing me. I hop to my feet and raise my fists. "Relax! You aren't the only one here who remembers two different worlds." She flips out of the tree and lands gracefully in front of me. "I remember a world with you as a hero, and then this one with you as a villain.

"Wait… How do you know-"

"What you're thinking?" She cuts me off. "Believe me, I'm just as confused as you are. Did you also happen to wake up with a headache?" I nod.

"I wonder if this has something to do with Shadow, Tails, and I fighting with Eggman in the other version of Mobius…" I comment. "I wonder if anyone else remembers the old world."

"Maybe. But we'll never know if we just stand around thinking about it…"


	2. Reunion

**Hello everybody! Welcome back to Parallel Universe 2! I'm sorry for taking so long(I got busy), but now it's finally here! Enjoy!**

Parallel Universe 2: Eggman's Invasion: Chapter 2: Reunion

-Milles' POV-

I stare at the screen, intent on watching the white bat and blue hedgehog on display. I watch them walking and chatting, heading for some unknown location.

"Can we get a microphone on this thing?" I complain. "I would REALLY like to know what they're saying."

"All in due time Miles." My dad, Doctor Eggman, responds. "I'll worry about that after I get this Chaos Emerald powering my machine." He smiles at me. "Thanks by the way for getting it for me."

"No problem." I stand up and stretch, then grab my black leather jacket from off of my chair. "I'm going to go for a walk around base. I just need to stretch my legs."

"Ok, be back soon." I walk outside the control room's door and start walking down the hall, letting my thoughts run free.

"I feel like dad uses me sometimes…" I mumble to myself. "I mean, I've helped him loads of times by improving his machines, gathering chaos emeralds, yet he never shows true gratitude." I sigh. "All he seems to show is a fake smile and an uncaring 'thanks.'" My thoughts start to drift to the blue hedgehog, Sonic. "I wonder why dad hates him so much anyway, considering how much he hates Sonic." I walk out of the base. "You know what, I think I'll go find Sonic and meet him!" My twin tails start spinning, and soon I'm in the air. "Maybe if I meet Sonic, I'll understand my dad better…"

-Eggman's POV-

I glance at the monitors and see a yellow fox flying away.

"What the-? Where's she going?" I gasp as Miles shrinks off into the distance, becoming a dot and disappearing. "I told that girl she could walk around the base, not leave entirely!" I slam my fist on the desk in anger. "She'll learn sooner or later that I'm not to be messed with…"

-Sonic's POV-

"So, let me get this straight:" I say to Rouge. "In this world, I'm a criminal known for mass jewel heists, Eggman STILL hates me, and to top it all off, I'm completely and utterly alone and presumed insane?" Rouge nods.

"That pretty much sums it up. My memories indicate that you've also been known to have severe cases of amnesia at random moments…" She sighs and scratches her head. "Probably a side effect of whatever you were doing in the old world… The weirdest part is that before you saw me, I saw you, and all of my previous memories came rushing back… Almost as if you caused some sort of memory restore…"

"Wait, then what about Shadow?" I ask. "When I ran into him, he didn't know the old me at all."

"Maybe it's because he's from Earth and not Mobius like we are?" Rouge shakes her head. "I don't know. It's all some sort of big-"

"SONIC!" I turn and see a pink hedgehog running towards me. I groan as I realize that she must've regained her memories. She snatches me in a hug that threatens to squeeze the life out of my body. "I'm so sorry for calling the police on you like that!" She apologizes. "As soon as I got a 'safe' distance away, I turned around and suddenly remembered everything- As if there was a world before this one."

"Yes Amy," I groan, and she lets go of me apologetically. "Rouge and I have been trying to figure out the same thing as well." I scratch my head. "I wonder where Tails is right now… If I have any hope of fixing any of this, it's going to be with her help." I notice a yellow fox flying in the distance. "Hey that must be Tails!" I turn to Rouge and Amy. "Sorry, but I've got a friend to see." And with that, I start running towards Tails.

-Miles' POV-

"Hmm… I could've sworn that he's around here somewhere…" I notice a blue streak heading in my general direction. "What the? Is that Sonic?" I start to descend. The blue streak suddenly stops, kicking up a huge cloud of dust, and startling me so that I fall the last few feet to the ground.

"Tails?" I look in the direction and see the outline of a hedgehog in the slowly clearing dust cloud. I quickly pick myself up and start walking towards the figure.

"Tails?" I mimic. "Are you seriously calling me by my tails?" The dust clears and I'm able to make out a blue hedgehog with white gloves, red and white shoes, and green eyes. I clutch at my head and collapse to the ground as a fierce pain shoots through my skull, causing memories of a previous life to be suddenly remembered.

"Tails!" I feel Sonic rush to my side. "Are you okay?" I open my eyes and look directly into his.

"No… I think…" I say, pretending to be weak.

"What is it, Tails?"

"I think…" I jump up suddenly, startling Sonic. "I'm going to be A-Okay!"

Sonic stares at me for a few seconds, then we both start laughing.

"That..." Sonic wheezes from the intense laughter. "That's got to be the best thing I've heard… All day…"

"What's going on anyway?" I hear Tails ask. "I don't remember anything about you, then suddenly… Bam! I know everything about you! What happened here?"

"I think Egg-head somehow figured out how to change the world to be honest." I can almost see the gears turning in her head. "He must've used the Silver's time travel in combination with the Sol Emeralds to change time…" Tails snaps her fingers.

"I've got it! He couldn't have possibly changed time; he would've needed much more power." Tails explains. "Considering everything looks the same and not roboticized, he must've only been able to edit small areas, such as our first time meeting, or your reputation… He must've also been able to edit everyone's memories of you…"

"But how would that explain people regaining their memories of me? Rouge, Amy, and you only needed a good look of me to remember everything."

"I dunno… Maybe a possible side effect?" I shrug.

"Whatever it is, I'm sure we'll figure it out with a small chat with Baldy-McNosehair." Tails and I grin at the joke.

"Okay, but first let me get my plane." I blink at Tails.

"Plane? You mean the Tornado?" Tails nods. "Um… You are aware that it probably doesn't exist, right?"

"Huh? What do you mean?"

"Well, I originally took the plane from somewhere in Eggman's base then crash landed on South Island, your home, right?" Tails nods. "But if we didn't meet there, then the Tornado might still be broken down."

"Ah, true…" Tails scratches her head. "Well, to bring you with me to Eggman's base we'd need a plane, considering you hate being anywhere near water… If I had the parts, I could probably build a plane within a few hours…"

"But where could we get the parts?" I wonder aloud.

"I think I have an idea…"


	3. An Old Friend

Parallel Universe 2: Eggman's Invasion: Chapter 3: An Old Friend

-Tails' POV-

"This should be the place!" Sonic and I look at a rundown house that's sitting on the top of a cliff.

"Are you sure this is the place?" Questions Sonic. "This place seems kind of… Deserted…"

"No mistake about it. If I remember correctly, the person we're looking for lives just inside this house." I step towards the door and knock. The door slowly opens, revealing that the door was never truly shut. "Rotor? You in here?" I walk into the messy entrance. "Your door wasn't closed properly."

"Yes, I'm here…" A purple walrus yawns as he walks over to Sonic and I. "And I know about the door, I'll fix it when I get around to it."

"It's quite messy in here…" I observe, then grin. "But that's normal, isn't it?" Rotor scratches his head and breaks into a smile.

"Well, yeah… Even someone who's as smart as me can't seem to keep his place clean, am I right?"

"Now you're being cocky. Whoever said you were smart?" I joke. A cough from behind causes me to realize that I'm not just visiting an old friend. "Oop! Sorry about that Sonic!" I apologize.

"So this is Sonic the Hedgehog?" Rotor steps towards Sonic and walks around him, taking in every detail. "He certainly doesn't look like the criminal I've heard so much about…"

-Sonic's POV-

"Um… Anyway…" I say uncomfortably. "We need your help with something."

"What do you need?"

"We need a plane."

"A plane?" Rotor's face lights up. "Why didn't you just say so? I have all of the parts!" Tails smiles.

"And if I remember from last time…" Tails thinks aloud. "You owe me a favor, Mr. I'm-Going-To-Make-Out-With-Miles." Rotor blushes.

"H-hey!" Rotor sputters. "M-my friend tripped me, o-okay?!" Tails laughs.

"Sure she did." She taunts. "And I'm sure you enjoyed your little "accident", didn't you?" I stifle a laugh as I watch Rotor try to come up with an answer that won't get him into any more trouble.

"I- Uh… Ehm…" Rotor turns away and starts looking for plane pieces. "It… Er… Wasn't unpleasant…"

"So, what exactly happened?" I ask Tails when Rotor is out of earshot.

"Well…" Tails starts. "A few months back in this world I went to the beach with a girl named Sally Acorn, Rotor, and a guy named Antoine. We were all just chilling and hanging out when I asked Rotor for a soda, which he decided to get me one because he wanted one as well." She grins. "When he came back, however, Rotor tripped on Sally's leg by accident while handing me the soda, and you can probably figure out what happened from there."

"That's got to be the best story I've ever heard!" I shake my head and smile. "Did Sally trip Rotor on purpose?"

"I honestly don't know." Tails shrugs. "It probably wasn't intentional, but after seeing what happened she probably wanted to take credit wherever possible."

"Okay guys, I found all of the parts!" Rotor walks in. "Luckily for you guys I already had a partially disassembled biplane in my garage. Now, what do you need this plane for anyway?"

"We need it to crack the Eggman!" I grin and put my right fist into my left hand.

"Eggman?" Rotor looks at Tails. "Isn't Eggman your father, Miles?" Tails shrugs.

"Well, yeah…"

"Then why do you want to take him out?"

"Well, it's a long story… Let's just leave it at there was basically an alternate form of this world where Sonic and I, along with some friends fight with Eggman constantly, then he found a way to change everyone's memories of just about everything."

"Um… Okay?" Rotor then looks at a blueprint. "Anyway, I've got a blueprint that I created of the biplane just in case you need it." He walks towards the door. "I've got to go pick up some important items, so I'll leave you guys some space." Rotor walks out the door and closes it.

"Hm…" Tails looks at the blueprint carefully. "This looks just like…" I take a look at the blueprint and gasp.

"It looks just like the Tornado!" I say. Tails nods.

"This should be pretty easy then…" She says to herself thoughtfully. "It may be missing a few parts, but the main body could be easily put back together within an hour."

"He left the wings alone." I observe. "Those are probably the hardest to assemble…"

"Anyway," Tails stands up and picks up some pieces. "I need to start working on this if we want to get to Eggman as quickly as possible." She walks into the garage, leaving me alone. I sit down on the couch and slowly start to drift off…

_"Huh?" I look around the white room and search for a door. "Where am I?" I stand up and begin feeling around the walls for some sort of hidden switch. "Wait…" I facepalm. "What do you need Silver?"_

_ "Hey! You sound like you're displeased to see me!" I turn around to see the white hedgehog in question._

_ "Sorry, it's just that every time you do this, something bad happens, first with the chili dog stand, then with Tails' secret, what do you need to tell me this time?"_

_ "I came to tell you that Eggman's planning something." I roll my eyes._

_ "When isn't he planning something?"_

_ "Remember how Eggman used my power combined with the Sol Emeralds to change the world a little bit?" I nod. "Well, he still has me in his base along with the Sol Emeralds. Starting with the Chaos Emerald that Tails stole, I think he's trying to change the world again- But this time even bigger, maybe even changing YOUR timeline."_

_ "What?" I stare at Silver in shock. "But… Would the Chaos Emeralds really give him enough power?"_

_ "From what I've seen, I don't know. I've tried to contact with Shadow, but for whatever reason I can't."_

_ "It might be because he might not remember you…"_

_ "Exactly. For me to contact with dreams, the person I'm contacting has to actually know who I am." Silver's form flickers. "Anyway, I'm running out of energy keeping this dream up." Silver's voice gradually starts to become more distant. "If you can… Shadow… Knows… Probably…"_

_ "Silver!" I yell and start running towards him, then everything goes dark._

I wake up in a cold sweat and fall off of the couch. I look around and see Tails standing over me in concern.

"Sonic? Are you okay?" She asks. I nod and sit back on the couch, calming down a little.

"That was Silver." I explain. "Apparently he's still in Eggman's base with the Sol Emeralds. According to him, Eggman might be trying to change even more with the Chaos Emeralds."

"Shoot…" I hear Tails mutter, then she turns back to me. "We have to stop him as quickly as possible. If he has the Sol Emeralds and manages to combine their power with the Chaos Emeralds…" She trails off.

"There's no telling what could happen." I finish for her, and she nods. "Did you fix the Tornado?" Another nod. I jump up off the couch and land next to the door. "Then let's go confront Egg-head before we do anything else!" We run outside and I hop onto the Tornado's wing while Tails sits at the controls. Within a minute we're up in the air and flying towards Eggman's base.

-Eggman's POV-

"I'll ask you again, hedgehog, who did you contact?!" The white hedgehog in front of me shakes his head.

"What makes you think I can contact anyone?" He asks.

"Well," I start. "Considering that you seemed to be concentrating and I could've sworn I saw your hands glowing, I'd say it was a telepathic link."

"IT'S NO USE!" Silver yells. "I won't tell you anything Eggman!" I smirk evilly.

"Oh well, it doesn't matter." I turn to my machine which has the 7 Sol Emeralds and 6 Chaos Emeralds inside. "Thanks to my new drones, it won't matter anyway. From the data I've received, CHAOS-013 has already found the last one and is now bringing it here."

"Er…" Silver starts. "THAT'S ALSO NO USE!" he yells, and I press a button that sound proofs his cell.

"Stupid loud rodent." I mutter to myself as I put the finishing touches onto my machine that will certainly allow me complete control of time.


End file.
